Blog by James Millington, PhD

Tag: Forests

When you haven’t done something for a while it’s often best not to rush straight back in at the intensity you were at before. So here’s a nice easy blog to get me going again (not that I was blogging intensely before!).

I didn’t blog about it at the time (unsurprisingly), but back in late June 2013 I went to visit a colleague of mine in Madrid, Dr Francisco Seijo. Francisco and I met back at something I did blog about, the 2009 US-IALE conference in Snowbird. Since then we’ve been discussing how we can use the idea of coupled-human and natural systems to investigate Mediterranean landscapes.

Example of Traditional Fire Knowledge. The ‘pile-burning’ technique involves raking, piling and igniting leaves. This contrasts with ‘a manta’ broadcast burning in which leaves and ground litter are burned across larger areas. Photos by the authors of the paper.

After a brief field visit by me, an interview campaign by Francisco, collection of secondary data from other sources (aerial photography and official fire statistics) and some desk analysis, we recently published our first paper on the work. Entitled Forgetting fire: Traditional fire knowledge in two chestnut forest ecosystems of the Iberian Peninsula and its implications for European fire management policy, and published in the journal Land Use Policy, the article presents the results of our mixed-methods and interdisciplinary approach. Building on Francisco’s previous examination of ‘pre-industrial anthropogenic fire regimes’ we to to investigate differences between the fire regimes and management approaches of chestnut forest ecosystems in two municipalities in central Spain. In the paper we also discuss ideas of Traditional Ecological Knowledge (TEK), the related idea of Traditional Fire Knowledge (TFK), and discuss them in light of contemporary fire management approaches in Europe.

The full abstract is below with links to the paper. I’ll stop here now as this rate of blogging it making me quite dizzy (but hopefully I’ll be back for more soon).

Human beings have used fire as an ecosystem management tool for thousands of years. In the context of the scientific and policy debate surrounding potential climate change adaptation and mitigation strategies, the importance of the impact of relatively recent state fire exclusion policies on fire regimes has been debated. To provide empirical evidence to this ongoing debate we examine the impacts of state fire exclusion policies in the chestnut forest ecosystems of two geographically neighbouring municipalities in central Spain, Casillas and Rozas de Puerto Real. Extending the concept of ‘Traditional Ecological Knowledge’ to include the use of fire as a management tool as ‘Traditional Fire Knowledge’ (TFK), we take a mixed-methods and interdisciplinary approach to argue that currently observed differences between the municipalities are useful for considering the characteristics of “pre-industrial anthropogenic fire regimes” and their impact on chestnut forest ecosystems. We do this by examining how responses from interviews and questionnaire surveys of local inhabitants about TFK in the past and present correspond to the current biophysical landscape state and recent fire activity (based on data from dendrochronological analysis, aerial photography and official fire statistics). We then discuss the broader implications of TFK decline for future fire management policies across Europe particularly in light of the published results of the EU sponsored FIRE PARADOX research project. In locations where TFK-based “pre-industrial anthropogenic fire regimes” still exist, ecosystem management strategies for adaptation and mitigation to climate change could be conceivably implemented at a minimal economic and political cost to the state by local communities that have both the TFK and the adequate social, economic and cultural incentives to use it.

Just this week our first year undergraduates had their fieldweek, with lots of geography-related activities across London. For the physical geography activities we headed up to Heartwood Forest, the largest new native forest in England (near Sandridge in Hertfordshire). A nice video from last year’s trip is below.

As you can see from the video, currently much of the ‘forest’ looks more like fields than what would be considered forest in Michigan, but the 600,000 trees being planted by volunteers will grow over the coming years to change that. There are three existing ancient woodlands (covering 45 acres) in the entire 858 acre (347 ha) area the Woodland Trust have acquired. Much of this area was previously agricultural land – the planted trees and newly created meadows will connect the existing woodland.

So there’s going to be some big ecological changes over the coming years as landscape changes. To keep track of changes in vegetation and animal populations volunteers from the Herefordshire Natural History Society (HNHS) have set up a monitoring group that regularly collect data on the growth of new trees, plants, mammals, birds and butterflies.

Similarly, some of the activities our first year undergrads undertook were to do ecological surveys of understory and overstory vegetation. Our students also did hillslope surveys and soil moisture monitoring, measured vertical wind speed profiles (to see how wind speed changes with height from the ground), explored the use of helium balloons and thermal cameras to make aerial photographs and other observations, and learned how to use global positioning system (GPS) units. The students seemed to enjoy the day at Heartwood, and the entire fieldweek for that matter, as you can see from their activities on Twitter (we use the #kclfield hastag to associate tweets with our field activities).

Tweets about “#KCLfield”!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?’http’:’https’;if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+”://platform.twitter.com/widgets.js”;fjs.parentNode.insertBefore(js,fjs);}}(document,”script”,”twitter-wjs”);Over the coming years we hope to expand our students’ field activities at Heartwood to our third year undergraduate and taught Master’s students. In particular, we hope that dissertation research by these students will be able to contribute to the efforts of the Heartwood monitoring group, to collect data and investigate questions of ecological interest. For example, to analyse presence/absence data for mammals like woodmice, we might use statistical modelling techniques like those I used to examine neotropical bird populations in Michigan.

“The model simulates the initial height of the tallest saplings 10 years following gap creation (potentially either advanced regeneration or gap colonizers), and grows them until they are at least 7 m in height when they are passed to FVS for continued simulation. Our approach does not aim to produce a thorough mechanistic model of regeneration dynamics, but rather is one that is sufficiently mechanistically-based to allow us to reliably predict regeneration for trees most likely to recruit to canopy positions from readily-collectable field data.”

In the model we assume that each forest gap contains space for a given number of 7m tall trees. For each of these spaces in a gap, we estimate the probability that it is in one of four states 10 years after harvest:

occupied by a 2m or taller sugar maple tree (SM)

occupied by a 2m or taller ironwood tree (IW)

occupied by a 2m or taller tree of another species (OT)

not occupied by a tree 2m or taller (i.e., empty, ET)

To estimate the probabilities of these states for each of the gap spaces, given different environmental conditions, we use regression modelling for composition data:

“The gap-level probability for each of the four gap-space states (i.e., composition probabilities) is estimated by a regression model for composition data (Aitchison, 1982 and Aitchison, 1986). Our raw composition data are a vector for each of our empirical gaps specifying the proportion of all saplings with height >2 m that were sugar maple, ironwood, or other species (i.e., SM, IW, and OT). If the total number of trees with height >2 m is denoted by t, the proportion of empty spaces (ET) equals zero if t > n, otherwise ET = (n − t)/n. These raw composition data provide information on the ratios of the components (i.e., gap-space states). The use of standard statistical methods with raw composition data can lead to spurious correlation effects, in part due to the absence of an interpretable covariance structure (Aitchison, 1986). However, transforming composition data, for example by taking logarithms of ratios (log-ratios), enables a mapping of the data onto the whole of real space and the use of standard unconstrained multivariate analyses (Aitchison and Egozcue, 2005). We transformed our composition data with a centred log-ratio transform using the ‘aComp’ scale in the ‘compositions’ package (van den Boogaart and Tolosana-Delgado, 2008) in R (R Development Core Team, 2009). These transformed data were then ready for use in a standard multivariate regression model. A centred log-ratio transform is appropriate in our case as our composition data are proportions (not amounts) and the difference between components is relative (not absolute). The ‘aComp’ transformation uses the centred log-ratio scalar product (Aitchison, 2001) and worked examples of the transformation computation can be found in Tolosana-Delgado et al. (2005).”

One of the things I’d like to highlight here is that the R script I wrote to do this modelling is available online as supplementary material to the paper. You can view the R script here and the data we ran it for here.

If you look at the R script you can see that for each gap, proportions of gap-spaces in the four states predicted by the regression model are interpreted as the probability that gap-space is in the corresponding state. With these probabilities we predict the state of each gap space by comparing a random value between 0 and 1 to the cumulative probabilities for each state estimated for the gap. Table 1 in the paper shows an example of this.

With this model setup we ran the model for scenarios of different soil conditions, deer densities, canopy openness and Ironwood basal area (the environmental factors in the model that influence regeneration). The results for these scenarios are shown in the figure below.

Hopefully this gives you an idea about how the model works. The paper has all the details of course, so check that out. If you’d like a copy of the paper(s) or have any questions just get in touch (email or @jamesmillington on twitter)

Millington, J.D.A., Walters, M.B., Matonis, M.S. and Liu, J. (2013) Filling the gap: A compositional gap regeneration model for managed northern hardwood forests Ecological Modelling 253 17–27 doi: 10.1016/j.ecolmodel.2012.12.033Regeneration of trees in canopy gaps created by timber harvest is vital for the sustainability of many managed forests. In northern hardwood forests of the Great Lakes region of North America, regeneration density and composition are highly variable because of multiple drivers that include browsing by herbivores, seed availability, and physical characteristics of forest gaps and stands. The long-term consequences of variability in regeneration for economic productivity and wildlife habitat are uncertain. To better understand and evaluate drivers and long-term consequences of regeneration variability, simulation models that combine statistical models of regeneration with established forest growth and yield models are useful. We present the structure, parameterization, testing and use of a stochastic, regression-based compositional forest gap regeneration model developed with the express purpose of being integrated with the US Forest Service forest growth and yield model ‘Forest Vegetation Simulator’ (FVS) to form an integrated simulation model. The innovative structure of our regeneration model represents only those trees regenerating in gaps with the best chance of subsequently growing into the canopy (i.e., the tallest). Using a multi-model inference (MMI) approach and field data collected from the Upper Peninsula of Michigan we find that ‘habitat type’ (a proxy for soil moisture and nutrients), deer density, canopy openness and basal area of mature ironwood (Ostrya virginiana) in the vicinity of a gap drive regeneration abundance and composition. The best model from our MMI approach indicates that where deer densities are high, ironwood appears to gain a competitive advantage over sugar maple (Acer saccharum) and that habitat type is an important predictor of overall regeneration success. Using sensitivity analyses we show that this regeneration model is sufficiently robust for use with FVS to simulate forest dynamics over long time periods (i.e., 200 years).

Millington, J.D.A., Walters, M.B., Matonis, M.S. and Liu, J. (2013) Modelling for forest management synergies and trade-offs: Northern hardwood tree regeneration, timber and deer Ecological Modelling 248 103–112 doi: 10.1016/j.ecolmodel.2012.09.019In many managed forests, tree regeneration density and composition following timber harvest are highly variable. This variability is due to multiple environmental drivers – including browsing by herbivores such as deer, seed availability and physical characteristics of forest gaps and stands – many of which can be influenced by forest management. Identifying management actions that produce regeneration abundance and composition appropriate for the long-term sustainability of multiple forest values (e.g., timber, wildlife) is a difficult task. However, this task can be aided by simulation tools that improve understanding and enable evaluation of synergies and trade-offs between management actions for different resources. We present a forest tree regeneration, growth, and harvest simulation model developed with the express purpose of assisting managers to evaluate the impacts of timber and deer management on tree regeneration and forest dynamics in northern hardwood forests over long time periods under different scenarios. The model couples regeneration and deer density sub-models developed from empirical data with the Ontario variant of the US Forest Service individual-based forest growth model, Forest Vegetation Simulator. Our error analyses show that model output is robust given uncertainty in the sub-models. We investigate scenarios for timber and deer management actions in northern hardwood stands for 200 years. Results indicate that higher levels of mature ironwood (Ostrya virginiana) removal and lower deer densities significantly increase sugar maple (Acer saccharum) regeneration success rates. Furthermore, our results show that although deer densities have an immediate and consistent negative impact on forest regeneration and timber through time, the non-removal of mature ironwood trees has cumulative negative impacts due to feedbacks on competition between ironwood and sugar maple. These results demonstrate the utility of the simulation model to managers for examining long-term impacts, synergies and trade-offs of multiple forest management actions.

Nearing the end of 2012 and the total number of posts on this blog has been even fewer this year than in 2011. At least I have been tweeting a bit more of late. Here’s a quick round-up of activities and publications since my last post with a look at some of what’s going on in 2013.

The Geoforumpaper on narrative explanation of simulation modelling is now officially published, as is the first of twoEcological Modelling papers on the Michigan forest modelling work. Citations and abstract for both are below, and are included on my updated publications list. I’ll post more details and info on each in the New Year (promise!). I’ll likely wait to summarise the Michigan paper until the second paper of that couplet is published – hopefully that won’t be too long as it’s now going through the proofs stage.

The proceedings for the iEMSs conference I attended in Leipzig, Germany, this summer are now online. That means that the two papers I presented there are also available. One paper was on the use of social psychology theory for modelling farmer decision-making, and the model I discuss in that paper is available for you to examine. The other paper was a standpoint contribution to a workshop on the place of narrative for explaning decision-making in agent-based models. From that workshop we’re working on a paper to be published in Environmental Modelling and Software about model description methods for agent-based models. More on that next year too hopefully.

In one of my earlier posts this year I talked about agent-based modelling spatial patterns of school choice (I’ll get the images for that post online again soon… maybe). I’ve managed to write up the early stages of that work and have submitted it to JASSS. We’ll see how that goes down. I hope to continue on that work in the new year also, possibly while in New Zealand at the University of Auckland. I’ll be in Auckland visiting and working with George Perry and David O’Sullivan, with whom I published the recent Geoforum paper (highlighted above). On the way to New Zealand I’ll be stopping off in Los Angeles for the Association of American Geographers conference which I haven’t been to previously and which should be interesting.

So that’s it for 2012. A New Year’s resolution for 2013 – post at least once every month on this blog! Especially from Down Under.

Happy Holidays!

AbstractsMillington, J.D.A., O’Sullivan, D., Perry, G.L.W. (2012) Model histories: Narrative explanation in generative simulation modellingGeoforum43 1025–1034 The increasing use of computer simulation modelling brings with it epistemological questions about the possibilities and limits of its use for understanding spatio-temporal dynamics of social and environmental systems. These questions include how we learn from simulation models and how we most appropriately explain what we have learnt. Generative simulation modelling provides a framework to investigate how the interactions of individual heterogeneous entities across space and through time produce system-level patterns. This modelling approach includes individual- and agent-based models and is increasingly being applied to study environmental and social systems, and their interactions with one another. Much of the formally presented analysis and interpretation of this type of simulation resorts to statistical summaries of aggregated, system-level patterns. Here, we argue that generative simulation modelling can be recognised as being ‘event-driven’, retaining a history in the patterns produced via simulated events and interactions. Consequently, we explore how a narrative approach might use this simulated history to better explain how patterns are produced as a result of model structure, and we provide an example of this approach using variations of a simulation model of breeding synchrony in bird colonies. This example illustrates not only why observed patterns are produced in this particular case, but also how generative simulation models function more generally. Aggregated summaries of emergent system-level patterns will remain an important component of modellers’ toolkits, but narratives can act as an intermediary between formal descriptions of model structure and these summaries. Using a narrative approach should help generative simulation modellers to better communicate the process by which they learn so that their activities and results can be more widely interpreted. In turn, this will allow non-modellers to foster a fuller appreciation of the function and benefits of generative simulation modelling.

Millington, J.D.A., Walters, M.B., Matonis, M.S. and Liu, J. (2013) Modelling for forest management synergies and trade-offs: Northern hardwood tree regeneration, timber and deerEcological Modelling248 103–112 In many managed forests, tree regeneration density and composition following timber harvest are highly variable. This variability is due to multiple environmental drivers – including browsing by herbivores such as deer, seed availability and physical characteristics of forest gaps and stands – many of which can be influenced by forest management. Identifying management actions that produce regeneration abundance and composition appropriate for the long-term sustainability of multiple forest values (e.g., timber, wildlife) is a difficult task. However, this task can be aided by simulation tools that improve understanding and enable evaluation of synergies and trade-offs between management actions for different resources. We present a forest tree regeneration, growth, and harvest simulation model developed with the express purpose of assisting managers to evaluate the impacts of timber and deer management on tree regeneration and forest dynamics in northern hardwood forests over long time periods under different scenarios. The model couples regeneration and deer density sub-models developed from empirical data with the Ontario variant of the US Forest Service individual-based forest growth model, Forest Vegetation Simulator. Our error analyses show that model output is robust given uncertainty in the sub-models. We investigate scenarios for timber and deer management actions in northern hardwood stands for 200 years. Results indicate that higher levels of mature ironwood (Ostrya virginiana) removal and lower deer densities significantly increase sugar maple (Acer saccharum) regeneration success rates. Furthermore, our results show that although deer densities have an immediate and consistent negative impact on forest regeneration and timber through time, the non-removal of mature ironwood trees has cumulative negative impacts due to feedbacks on competition between ironwood and sugar maple. These results demonstrate the utility of the simulation model to managers for examining long-term impacts, synergies and trade-offs of multiple forest management actions.

This blog has been seriously neglected over the last six months, so there’s a lot of catching up to do here.

There’s lots of conferences and papers to list, but first I should highlight the slight difference in look of this blog and the entire website. I recently decided I was going to switch to Google sites to host www.landscapemodelling.net and move this blog from WordPress to Blogger (for multiple reasons I won’t go into here). The website is lacking many of the pages from its previous guise and the NetLogo models have been moved to openABM.org. I’m continuing to add the old (and maybe some new) content to the website but that’s likely to be a slow process (particularly given how long it’s taken me to get to write this post!). The link structure of the blog pages has changed – I think I’ve managed to change most links but there may still be some that are broken (if you find any please let me know). Many of the images are also currently missing – I’ll get to re-inserting those sometime…

I’ve managed to get to quite a few conferences this year in the US, UK and Germany.A particular highlight was getting to see my old PhD advisor George Perry in the US. George was on sabbatical at Harvard Forest and he invited me to the forest to give a seminar. It was also great to attend the 4th USFS FVS conference in Fort Collins, CO and to be one of the only four or so international attendees. There’s a list below of all the conference presentations I gave with links to the conference websites.

I’ve also been working hard to get a few papers published. The paper I’ve been working on with George and David O’Sullivan on the narrative properties of generative simulation models (i.e., agent-based models and the like) has now been accepted and is in press at Geoforum. Two papers I have been working on related to my work in Michigan have also been accepted, subject to corrections, by Ecological Modelling. The papers are closely linked, with one describing the northern hardwood forest gap regeneration model we developed and the second showing how that model can be used in the integrated model to examine trade-offs and synergies in managing for both timber and deer in the forests. The current (provisional) citations for the three papers are below. When all are available online and in print I’ll post again here with the abstracts and links to the full text (and likely tweet the links before I blog!)

Although I’ve been working on new ideas since leaving Michigan and returning to London about a year ago, there’s still lots to do to examining alternative forest management strategies.

Several years ago we set out to develop a simulation model that could be used to investigate the effects of interactions between timber harvest and deer browse disturbances on economic productivity and wildlife habitat. We’ve already published several papers on this work, but just before Christmas we submitted a manuscript to Ecological Modelling entitled ‘Modelling for forest management synergies and trade-offs: Tree regeneration, timber and wildlife’. In the manuscript we report error analyses of the full simulation model (which uses the USFS Forest Vegeation Simulator) and use the model to investigate scenarios of different timber and deer management actions. Our results indicate that greater harvest of commercially low-value ironwood and lower deer densities significantly increase sugar maple regeneration success over the long term.

I expect we’ll also report some of these results at the Fourth Forest Vegetation Simulator (FVS) Conference to be held in April this year in Fort Collins, CO. Our abstract, entitled ‘Investigating combined long-term effects of variable tree regeneration and timber management on forest wildlife and timber production using FVS’, has been accepted for oral presentation. It would be great to be there myself to present the paper and discuss things with other FVS experts, but I’m not sure if that will be possible. If it’s not, Megan Matonis will present as, handily, she’s currently doing her PhD in that neck of the woods at Colorado State University.

In the meantime, Megan and I are in the process of finishing off a different manuscript describing the mesic conifer planting experiment we did in Michigan. In that experiment we planted seedlings of white pine (Pinus strobus), hemlock (Tsuga canadensis), and white spruce (Picea glauca) in northern hardwood stands with variable deer densities and then monitored browse on the seedlings over two years. We found that damage to pine and hemlock seedlings was inversely related to increasing snow depth, and our data suggest a positive relationship between hemlock browse and deer density. These results suggest that hemlock restoration efforts will not be successful without protection from deer. Hopefully we’ll submit the manuscript, possibly to the Northern Journal of Applied Forestry, in the next month or so.

All of this work has been pursued with management in mind, so it was nice this week to receive a call from Bob Doepker, a manager at the Michigan Department of Natural Resources with whom we worked to co-ordinate data collection and establish key research questions. Bob had some questions about the details and implications of our previous findings for deer habitat, tree regeneration and how they should be managed. It was good to catch up, and no doubt our ongoing work will continue to contribute to contemporary management understanding and planning.

These last few days I’ve been up in Edinburgh visiting folks at the Forestry Commission’s Northern Research Station to discuss the socio-ecological modelling of potential woodland creation I’ve been working on recently. I also got to talk with Derek Robinson at the University of Edinburgh about some of these issues. Everyone seemed interested in what I’ve been doing, particularly with the ideas I’ve been bouncing around relating to the work Burton and Wilson have been doing on post-productivist farmer self-identities, how these self-identities might change, how they might influence adoption of woodland planting and how we might model that. For example, I think an agent-based simulation approach might be particularly useful for exploring what Burton and Wilson term the ‘‘temporal discordance’ in the transition towards a post-productivist agricultural regime”. And I also think there’s potential to tie it in with work like my former CSIS colleague Xiaodong Chen has been doing using agent-based approaches to model the effects of social norms on enrollment in payments for ecosystem services (such as woodland creation).

I was away on holiday for a couple of weeks after the RGS. On returning, I’ve been preparing for King’s Geography tutorials with the incoming first year undergraduates. The small groups we’ll be working will allow us to discuss and explore critical thinking and techniques about issues and questions in physical geography. Looking forward a busy autumn term!